pipeline.json

{   
    "name": "Test1",
    "description": "This pipeline can be performed to test FLENP, see README for more info.",
    "author": "FLENP",
    "url": "https://github.com/pietrocinaglia/flenp",
    "help": "Pipeline for testing.",
    "pipeline": {
        "p1": {
            "params": "SAMPLES_DIR,P1_TIME",
            "statement": "foreach OBJ in {{WORKSPACE}}/{{SAMPLES_DIR}}",
            "parallel": false,
            "steps": [
                {
                    "name": "Mapping Sample on Reference Genome [.sam]",
                    "description": "- Output: .sam",
                    "cmd": "./modules/test {{OBJ}}_1.fq.gz_AND_{{OBJ}}_2.fq.gz {{P1_TIME}}"
                },{
                    "name": "Sorting",
                    "description": "- Output: .bam",
                    "cmd": "./modules/test {{OBJ}}.sam {{P1_TIME}}"
                }
            ]
        },
        "p2": {
            "params": "P2_PAR1,P2_TIME",
            "steps": [
                {
                    "name": "Merging All Transcripts",
                    "description": "",
                    "cmd": "./modules/test {{P2_PAR1}} {{P2_TIME}}"
                }
            ]
        }
    }
}